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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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Electron Microscope Tomography and Single-particle Reconstruction01:07

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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...
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Overview of Electron Microscopy01:25

Overview of Electron Microscopy

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The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.
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Related Experiment Video

Updated: May 7, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

Ingvar Lagerstedt1, William J Moore, Ardan Patwardhan

  • 1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, United Kingdom.

Journal of Structural Biology
|October 12, 2013
PubMed
Summary

The Protein Data Bank in Europe (PDBe) offers new web tools for easy 3D electron microscopy (3DEM) data analysis. These tools visualize and validate structures from the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB) without software installation.

Keywords:
3DEMEM VTCEMDBElectron Microscopy Data BankElectron Microscopy Validation Task ForceElectron microscopyElectron tomographyFSCFourier Shell CorrelationMacromolecular structureOAVOMEOME Remote ObjectsOMEROOpen Astex ViewerOpen Microscopy EnvironmentPDBPDBeProtein Data BankProtein Data Bank in EuropeThree-Dimensional Electron MicroscopyVisualisationWorldwide Protein Data BankwwPDB

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • The Protein Data Bank in Europe (PDBe) manages crucial structural biology data.
  • 3D electron microscopy (3DEM) data requires specialized tools for visualization and analysis.
  • Accessibility to 3DEM data in archives like EMDB and PDB can be limited by software and data size requirements.

Purpose of the Study:

  • To develop user-friendly, web-based tools for visualizing and analyzing 3DEM structures.
  • To enable both experts and non-experts to access and interpret 3DEM data from PDBe.
  • To facilitate the assessment of 3DEM map and model quality without specialized software.

Main Methods:

  • Development of a volume viewer for 3D visualization of maps, tomograms, and models.
  • Implementation of a slice viewer for examining 2D slices of tomographic reconstructions.
  • Creation of visual analysis pages for map, tomogram, and model validation.

Main Results:

  • Successfully deployed web-based tools for 3DEM data visualization and analysis.
  • Tools provide insights into 3DEM structure content and quality.
  • Eliminated the need for specialized software installation and large data downloads.

Conclusions:

  • Web-based tools enhance accessibility and usability of 3DEM data.
  • PDBe tools empower a wider scientific community to engage with 3DEM structural information.
  • The development addresses technical challenges in presenting archived 3DEM data effectively.